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Abstract Background Endometriosis is a chronic, estrogen-dependent, benign condition, affecting 10–15% of women of reproductive age. It is associated with a prevalence of sexual dysfunction that is nearly twice as high as that seen in women with other benign gynecological conditions. Our study aimed to assess the effect of surgical intervention on sexual function, as measured by the FSFI (Female Sexual Function Index) score, in women with endometriosis compared to those with other benign gynecological conditions, both before and after surgery. Methods A comparative analysis was conducted at the Medical University of Vienna from 2015 to 2020. The study included patients suspected of having endometriosis, fibroids, adnexal cysts, and/or infertility. Based on findings during surgery, patients were categorized into two groups: those with endometriosis (n = 64) and control patients (n = 38). All participants completed the FSFI questionnaire before surgery and again 8 to 18 weeks after the operation. Results No significant differences were observed in the preoperative FSFI scores between the endometriosis patients and the control group. Similarly, no significant differences were found between the two groups in postoperative scores. However, in women diagnosed with endometriosis, surgical removal of endometriotic lesions significantly increased their full-scale FSFI score, and resulted in a significant improvement in the areas “desire” and “satisfaction”. Improvements were noted in all other areas as well, though they were not statistically significant. Conclusions Our research indicates that the surgical removal of endometriotic lesions can lead to an improvement in sexual function, as measured by the FSFI, within 8 to 18 weeks post-surgery. This improvement was not observed in the control group, which underwent surgery for other benign gynecological issues.